X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8J2V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2980.1 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate pH 6.5, 15% w/v PEG 6000
Crystal Properties
Matthews coefficientSolvent content
359.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.13α = 90
b = 170.39β = 93.39
c = 152.13γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.987SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.148.5378.440.9946.77.179381
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.210.10.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT8J2V3.148.5362884295374.270.259390.25630.31784RANDOM75.064
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
8.9-0.55-11.953.05
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined19.383
r_dihedral_angle_3_deg18.802
r_mcangle_it11.693
r_dihedral_angle_2_deg11.239
r_scbond_it8.221
r_dihedral_angle_1_deg8.08
r_mcbond_it7.435
r_angle_refined_deg2.016
r_chiral_restr0.287
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined19.383
r_dihedral_angle_3_deg18.802
r_mcangle_it11.693
r_dihedral_angle_2_deg11.239
r_scbond_it8.221
r_dihedral_angle_1_deg8.08
r_mcbond_it7.435
r_angle_refined_deg2.016
r_chiral_restr0.287
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25467
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms322

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing